Being as a plant of cross-pollination; the cultivar identification of alfalfa (Medicago sativa L.) is more difficult than other self-pollination plant because of the admixture genotypes within a cultivar. A preliminary study on alfalfa cultivar identification was conducted on native cultivars, bred cultivars, and cross cultivars using SSR markers. The results suggest that some nonspecific bands were avoided by using denatured gels for the separating of PCR products; the gene frequency of l4Sbp band of AFcal loci was much higher in Longmu series cultivars than that in other alfalfa cultivars, by which Longmu cultivars were identified among alfalfa cultivars. However, the gene frequency differences could not be used for other cultivar identification, because the differences among other alfalfa cultivars were small. Thus, it was very difficult to identify all alfalfa cultivars by using limited SSR markers. Some alfalfa cultivars could be identified by using the molecular marker associated with a specific trait of the cultivar.